There was a recent thread on the mrtrix forums that said that we should actually be running dweidenoise after eddy correction, and while searching for that post I came across this one and thought I’d link to the answer for what it’s worth (even though it’s a year later): Eddy/topup on denoised data
From that thread, someone posted “part of a discussion with Jesper Anderson (he is one of the authors of eddy)”:
Yes, I don’t recommend using denoising prior to eddy. I have seen very poor results on denoised data. It tends to mean that one ends up with unrealistic estimates of hyperparameters for the Gaussian Process, making “everything” look like valid signal variance and nothing look like noise. It would also interfere with eddy_qc and lead to inflated estimates of CNR.
I would also have thought that any denoising would work much better after eddy, where for example outliers have been detected and corrected.